Initial release by KateSakharova · Pull Request #72 · nf-core/seqsubmit

KateSakharova · 2026-06-15T14:56:19Z

nf-core/seqsubmit v1.0.0 — Initial Release

This is the first release of nf-core/seqsubmit, a Nextflow pipeline for submitting sequence data to the European Nucleotide Archive (ENA).

What it does:

The pipeline supports four submission modes via dedicated workflows:

mags — Metagenome Assembled Genomes submission (GENOMESUBMIT)
bins — Metagenomic bins submission (GENOMESUBMIT)
metagenomic_assemblies — Assembly submission (ASSEMBLYSUBMIT)
reads — Raw sequencing reads submission (READSUBMIT)

Key features:

Automatic study registration with ENA when no existing study accession is provided
Support for public and private data submissions, including configurable release dates
Coverage calculation from reads when not provided directly (via coverm)
Completeness/contamination estimation and taxonomy inference for MAGs/bins (via CheckM2 and CAT_pack) when metadata is incomplete
Credentials handled securely via Nextflow secrets (ENA_WEBIN, ENA_WEBIN_PASSWORD)
Full nf-core compatibility: runs with conda, Docker, and Singularity

Workflows and modules

READSUBMIT — manifest generation and webin-cli submission for raw reads
ASSEMBLYSUBMIT — manifest generation and webin-cli submission for metagenomic assemblies
GENOMESUBMIT — metadata table generation, genome upload, and webin-cli submission for MAGs/bins
Local modules: REGISTERSTUDY, CREATE_READS_MANIFEST, GENERATE_ASSEMBLY_MANIFEST, GENOME_UPLOAD, ENA_WEBIN_CLI_WRAPPER, and supporting utility modules

…diagram

Add assemblysubmit workflow and --mode metagenomic_assemblies

RNA detection for genomes_submit

added checkm2 and coverm_genome

…thods for RNA detection and assembly coverage

Remove vulnerable PR-comment artifact pattern

github-actions · 2026-07-24T14:56:18Z

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 4.0.3.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the Synchronisation documentation.

github-actions · 2026-07-24T14:57:36Z

`nf-core pipelines lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 361e07b

+| ✅ 253 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   4 tests had warnings |!

Details

❗ Test warnings:

readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/seqsubmit/seqsubmit/lint_results.md: _* pipeline_if_empty_null - No ifEmpty(null) strings found
_

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/igenomes_ignored.config
files_exist - File is ignored: .github/workflows/linting_comment.yml
nextflow_config - Config variable ignored: params.input
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: assets/nf-core-seqsubmit_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-seqsubmit_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-seqsubmit_logo_dark.png
container_configs - container_configs

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/nf-test.yml
files_exist - File found: .github/actions/get-shards/action.yml
files_exist - File found: .github/actions/nf-test/action.yml
files_exist - File found: .github/workflows/pr-comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-seqsubmit_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/CONTRIBUTING.md
files_exist - File found: docs/images/nf-core-seqsubmit_logo_light.png
files_exist - File found: docs/images/nf-core-seqsubmit_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: nf-test.config
files_exist - File found: tests/default.nf.test
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: modules.json
files_exist - File found: ro-crate-metadata.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-seqsubmit_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowSeqsubmit.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Found nf-schema plugin
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedHeaders
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version does not contain dev for release: 1.0.0
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.rrna_limit= 80.0
nextflow_config - Config default value correct: params.trna_limit= 18.0
nextflow_config - Config default value correct: params.checkm2_db_download_id= 14897628
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
nextflow_config - Config default value correct: params.upload_tpa= false
nextflow_config - Config default value correct: params.test_upload= true
nextflow_config - Config default value correct: params.is_private= false
nextflow_config - Config default value correct: params.webincli_mode= submit
nf_test_content - 'tests/reads_paired_end.nf.test' contains outdir parameter
nf_test_content - 'tests/reads_paired_end.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/reads_paired_end.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/assembly_no_study_complete_metadata.nf.test' contains outdir parameter
nf_test_content - 'tests/assembly_no_study_complete_metadata.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/assembly_no_study_complete_metadata.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_one_contig.nf.test' contains outdir parameter
nf_test_content - 'tests/mag_one_contig.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_one_contig.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_no_coverage_single_reads.nf.test' contains outdir parameter
nf_test_content - 'tests/mag_no_coverage_single_reads.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_no_coverage_single_reads.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/assembly_complete_metadata.nf.test' contains outdir parameter
nf_test_content - 'tests/assembly_complete_metadata.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/assembly_complete_metadata.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_no_coverage_paired_reads.nf.test' contains outdir parameter
nf_test_content - 'tests/mag_no_coverage_paired_reads.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_no_coverage_paired_reads.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_no_rna_presence.nf.test' contains outdir parameter
nf_test_content - 'tests/mag_no_rna_presence.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_no_rna_presence.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/default.nf.test' contains outdir parameter
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_no_study_complete_metadata.nf.test' contains outdir parameter
nf_test_content - 'tests/mag_no_study_complete_metadata.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_no_study_complete_metadata.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/assembly_no_coverage_single_reads.nf.test' contains outdir parameter
nf_test_content - 'tests/assembly_no_coverage_single_reads.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/assembly_no_coverage_single_reads.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/assembly_no_coverage_paired_reads.nf.test' contains outdir parameter
nf_test_content - 'tests/assembly_no_coverage_paired_reads.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/assembly_no_coverage_paired_reads.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_complete_metadata.nf.test' contains outdir parameter
nf_test_content - 'tests/mag_complete_metadata.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_complete_metadata.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_no_taxonomy.nf.test' contains outdir parameter
nf_test_content - 'tests/mag_no_taxonomy.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mag_no_taxonomy.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/assembly_one_contig.nf.test' contains outdir parameter
nf_test_content - 'tests/assembly_one_contig.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/assembly_one_contig.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
nf_test_content - 'nf-test.config' sets a testsDir
nf_test_content - 'nf-test.config' sets a workDir
nf_test_content - 'nf-test.config' sets a configFile
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/pr-comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
actions_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
actions_nf_test - '.github/workflows/nf-test.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 25.10.4, Config: 25.10.4
readme - README nf-core template version badge found.
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: pr-comment.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - assets/multiqc_config.yml found and not ignored.
multiqc_config - assets/multiqc_config.yml contains report_section_order
multiqc_config - assets/multiqc_config.yml contains export_plots
multiqc_config - assets/multiqc_config.yml contains report_comment
multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
local_component_structure - local subworkflows directory structure is correct 'subworkflows/local/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - FALINT found in conf/modules.config and Nextflow scripts.
modules_config - CATPACK_ADDNAMES_BINS found in conf/modules.config and Nextflow scripts.
modules_config - CATPACK_BINS found in conf/modules.config and Nextflow scripts.
modules_config - CATPACK_PREPARE found in conf/modules.config and Nextflow scripts.
modules_config - RENAME_FASTA_FOR_CATPACK found in conf/modules.config and Nextflow scripts.
modules_config - BARRNAP found in conf/modules.config and Nextflow scripts.
modules_config - TRNASCANSE found in conf/modules.config and Nextflow scripts.
modules_config - COUNT_RNA found in conf/modules.config and Nextflow scripts.
modules_config - CHECKM2_PREDICT found in conf/modules.config and Nextflow scripts.
modules_config - CHECKM2_DATABASEDOWNLOAD found in conf/modules.config and Nextflow scripts.
modules_config - COVERM_GENOME found in conf/modules.config and Nextflow scripts.
modules_config - COVERM_CONTIG found in conf/modules.config and Nextflow scripts.
modules_config - CREATE_ASSEMBLY_METADATA_CSV found in conf/modules.config and Nextflow scripts.
modules_config - CONCAT_METADATA found in conf/modules.config and Nextflow scripts.
modules_config - GENOME_UPLOAD found in conf/modules.config and Nextflow scripts.
modules_config - ENA_WEBIN_CLI_WRAPPER found in conf/modules.config and Nextflow scripts.
modules_config - REGISTERSTUDY found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 4.0.3
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.
version_consistency - Version tags are consistent: manifest.version = 1.0.0, nfcore_yml.version = 1.0.0
included_configs - Pipeline config includes custom configs.

Run details

nf-core/tools version 4.0.3
Run at 2026-07-30 14:47:35

github-actions · 2026-07-24T15:02:45Z

❌ nf-test failed with latest Nextflow version

Note

Tests with Nextflow's latest version failed but it will not cause a CI workflow failure.
Please check if the failure is expected with newer (edge-)releases of Nextflow or if it needs fixing.

❌ singularity | latest-everything | Shard 6/7

See the full run for details.

Co-authored-by: Sofia Ochkalova <61541445+ochkalova@users.noreply.github.com>

Change schema meta

Co-authored-by: Sofia Ochkalova <61541445+ochkalova@users.noreply.github.com>

Many different changes after review. Round 2

Fix/unify schema and docs

Important! Template update for nf-core/tools v4.0.3

jfy133

Preemptive ✅ when the approved #92 is merged

Updated resource settings reference for Nextflow configuration.

Fixes related to polishing for release

@matthdsm

Hi! I’m dismissing the review from @matthdsm since the requested changes have already been addressed, and he’s currently on holiday. We’d prefer not to delay the merge until he’s back. Hope that’s okay! Thanks a lot for your reviews, everyone :)

ochkalova and others added 30 commits March 6, 2026 15:38

docs: enhance README with detailed submission modes and add workflow …

38ab8e7

…diagram

fix: add '--outdir' option to README for output directory specification

a11a9d7

fix: rename test_assembly.conf to test.conf to satisfy nf-core linter

5803b9a

fix: patch fastavalidator module

39d7414

fix: bugfixes revealed by testing

6e31241

add more test cases for assemblysubmit

27b75b2

to be fixed: create empty test.config to satisfy linter

38e68d6

fix: update README for ENA submission examples

bd9a67f

Merge pull request #26 from nf-core/assembly_workflow

da12288

Add assemblysubmit workflow and --mode metagenomic_assemblies

WIP

c71b6f7

Template update for nf-core/tools version 3.4.1

b11c901

RNA detection subwf

e2843f4

Merge pull request #23 from nf-core/feature/rna_detection

f904453

RNA detection for genomes_submit

added checkm2 and coverm_genome

7bad55e

coverm works

de1670d

wip checkm2

7282a43

wip checkm2

e8850d1

checkm2 works

7411db6

minor issues

157f9a5

lint

7b074e8

minor README update

30b5fa4

rewrite count_rna.py to correctly count rRNA genes and add test

3458596

minor fixes

5d8bcfb

minor fixes

5c8088c

minor fixes

10de6cd

Merge pull request #34 from nf-core/feature/add-stats-genomesubmit

d6a32c1

added checkm2 and coverm_genome

remove license comments from count_rna.py

428ef6d

Installed the fasta_classify_catpack subworkflow

03eef16

Update documentation, add a new methods.md file detailing internal me…

c77aab2

…thods for RNA detection and assembly coverage

revert docs/README.md to satisfy linter

560a920

nf-core-bot and others added 2 commits July 24, 2026 16:33

Remove vulnerable PR-comment artifact pattern

f00aebf

Merge pull request #91 from nf-core/patch

6cfb2b5

Remove vulnerable PR-comment artifact pattern

KateSakharova and others added 8 commits July 27, 2026 11:56

change limits for coverage, completeness and contamination

d0e42be

Apply suggestion from @ochkalova

774f69c

Co-authored-by: Sofia Ochkalova <61541445+ochkalova@users.noreply.github.com>

Update subworkflows/local/genome_evaluation/main.nf

99970b6

Co-authored-by: Sofia Ochkalova <61541445+ochkalova@users.noreply.github.com>

Update conf/test_assembly_complete_metadata.config

1a322b6

Co-authored-by: Sofia Ochkalova <61541445+ochkalova@users.noreply.github.com>

Merge pull request #88 from nf-core/fix/meta_objects

fb2db68

Change schema meta

remove nr from main workflow and add to taxonomy subwf

2a0364c

Update docs and schemas for better descriptions

8af5f50

Co-authored-by: Sofia Ochkalova <61541445+ochkalova@users.noreply.github.com>

Merge pull request #86 from nf-core/fix/docs-review

645df17

Many different changes after review. Round 2

KateSakharova mentioned this pull request Jul 27, 2026

Fixes related to polishing for release #92

Merged

KateSakharova and others added 8 commits July 30, 2026 14:19

aligned docs and schemas

b4a5d48

docs polishing

68a9c22

Merge pull request #93 from nf-core/fix/unify-schema-and-docs

4f98fff

Fix/unify schema and docs

Merge branch '1.0.0' into nf-core-template-merge-4.0.3

3a74926

remove files_unchanged

19067fb

revert files_unchanged

decd115

Merge pull request #90 from nf-core/nf-core-template-merge-4.0.3

5673e5b

Important! Template update for nf-core/tools v4.0.3

Merge branch 'dev' into 1.0.0

fb3c3f1

jfy133 self-requested a review July 30, 2026 14:10

jfy133 approved these changes Jul 30, 2026

View reviewed changes

KateSakharova added 2 commits July 30, 2026 15:28

Revise resource settings guidance in usage documentation

670bdc6

Updated resource settings reference for Nextflow configuration.

Merge pull request #92 from nf-core/1.0.0

361e07b

Fixes related to polishing for release

vagkaratzas self-requested a review July 30, 2026 15:03

vagkaratzas approved these changes Jul 30, 2026

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KateSakharova merged commit 717fd19 into main Jul 31, 2026
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Initial release - #72

Initial release#72
KateSakharova merged 344 commits into
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KateSakharova commented Jun 15, 2026 •

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github-actions Bot commented Jul 24, 2026 •

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github-actions Bot commented Jul 24, 2026 •

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❗ Test warnings:

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github-actions Bot commented Jul 24, 2026

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KateSakharova commented Jun 15, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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github-actions Bot commented Jul 24, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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github-actions Bot commented Jul 24, 2026

❌ nf-test failed with latest Nextflow version

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KateSakharova commented Jun 15, 2026 •

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github-actions Bot commented Jul 24, 2026 •

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github-actions Bot commented Jul 24, 2026 •

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`nf-core pipelines lint` overall result: Passed ✅ ⚠️